#include <Molecule.hh>

Inheritance diagram for CASM::AtomPosition:

Detailed Description

Definition at line 56 of file Molecule.hh.

Public Types
typedef std::array< bool, 3 >	sd_type

typedef Eigen::Vector3d	vector_type

typedef vector_type::Index	size_type

Public Member Functions
	AtomPosition (const Lattice &init_lattice)

	AtomPosition (double elem1, double elem2, double elem3, std::string sp_name, const Lattice &init_lattice, COORD_TYPE mode, sd_type _SD_flag=sd_type{{false, false, false}})

bool	operator== (const AtomPosition &RHS) const

void	print (std::ostream &stream, const Coordinate &trans, int spaces, bool SD_is_on=false) const

AtomPosition &	apply_sym (const SymOp &op)

AtomPosition &	apply_sym_no_trans (const SymOp &op)

Coordinate_impl::FracCoordinate	frac ()
	Set the fractional coordinate vector. More...

const vector_type &	frac () const
	const Access the fractional coordinate vector More...

Coordinate_impl::FracCoordinateComponent	frac (size_type index)
	Set a component of the fractional coordinate vector. More...

const double &	frac (size_type index) const
	const Access a component of the fractional coordinate vector More...

const vector_type &	const_frac () const
	user override to force const Access the fractional coordinate vector More...

const double &	const_frac (size_type index) const
	user override to force const Access the fractional coordinate vector More...

Coordinate_impl::CartCoordinate	cart ()
	Set Cartesian coordinate vector and update fractional coordinate vector. More...

const vector_type &	cart () const
	const Access the Cartesian coordinate vector More...

Coordinate_impl::CartCoordinateComponent	cart (size_type index)
	Set a component of the Cartesian coordinate vector. More...

const double &	cart (size_type index) const
	const Access a component of the Cartesian coordinate vector More...

const vector_type &	const_cart () const
	user override to force const Access the Cartesian coordinate vector More...

const double &	const_cart (size_type index) const
	const Access a component of the Cartesian coordinate vector More...

Coordinate &	operator+= (const Coordinate &RHS)
	Positive translation of this coordinate by RHS.cart() More...

Coordinate &	operator-= (const Coordinate &RHS)
	Negative translation of this coordinate by RHS.cart() More...

Coordinate	operator- () const
	unary minus of this coordinate More...

bool	operator== (const Coordinate &RHS) const

bool	operator!= (const Coordinate &RHS) const

bool	almost_equal (const Coordinate &RHS, double tol) const

bool	compare (const Coordinate &RHS, double tol=TOL) const
	Returns true if this->min_dist(RHS)<tol. More...

bool	compare (const Coordinate &RHS, Coordinate &translation, double tol=TOL) const

bool	compare_type (const Coordinate &RHS) const
	Return true – Exists to allow duck-typing with Site. More...

bool	within ()

bool	within (Coordinate &translation)

bool	is_within () const
	Checks to see if coordinate is in the unit cell, but does not translate it. More...

int	voronoi_number () const

int	voronoi_number (const Lattice &cell) const

bool	voronoi_within ()
	Map coordinate into the voronoi cell using a lattice translation. More...

bool	voronoi_within (Coordinate &translation)

bool	is_lattice_shift (double tol=TOL) const
	Checks to see if coordinate is at a lattice translation with respect to the origin. More...

void	set_lattice (const Lattice &new_lat, COORD_TYPE mode)
	Change the home lattice of the coordinate, selecting one representation (either CART or FRAC) that remains invariant. More...

void	set_basis_ind (Index _basis_ind)
	Set basis Index. More...

Index	basis_ind () const
	Access basis Index. More...

const Lattice &	home () const
	Access the home lattice of the coordinate. More...

void	read (std::istream &stream, COORD_TYPE mode)

void	print (std::ostream &stream, COORD_TYPE mode, char term=0, int prec=7, int pad=5) const

void	print (std::ostream &stream, char term=0, int prec=7, int pad=5) const

void	print_axis (std::ostream &stream, COORD_TYPE mode, char term=0, int prec=7, int pad=5) const
	Print normalized vector. More...

double	dist (const Coordinate &neighbor) const
	distance (in Angstr) of neighbor from *this More...

double	min_dist (const Coordinate &neighbor) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	min_dist (const Coordinate &neighbor, Coordinate &translation) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	robust_min_dist (const Coordinate &neighbor) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	robust_min_dist (const Coordinate &neighbor, Coordinate &translation) const
	Returns distance (in Angstr) to nearest periodic image of neighbor. More...

double	min_dist2 (const Coordinate &neighbor, const Eigen::Ref< const Eigen::Matrix3d > &metric) const
	Finds same shift as min_dist but returns shift(CART).transpose()metricshift(CART) More...

jsonParser &	to_json (jsonParser &json) const

void	from_json (const jsonParser &json)

Static Public Member Functions
static Coordinate	origin (const Lattice &_home)
	construct a coordinate describing origin of _home lattice More...

Public Attributes
Specie	specie

sd_type	SD_flag

Member Typedef Documentation

typedef vector_type::Index CASM::Coordinate::size_type

inherited

Definition at line 37 of file Coordinate.hh.

typedef Eigen::Vector3d CASM::Coordinate::vector_type

inherited

Definition at line 36 of file Coordinate.hh.

Member Function Documentation

bool CASM::Coordinate::almost_equal	(	const Coordinate &	RHS,
		double	tol
	)		const

inherited

Definition at line 66 of file Coordinate.cc.

Index CASM::Coordinate::basis_ind ( ) const

inlineinherited

Access basis Index.

Definition at line 190 of file Coordinate.hh.

Coordinate_impl::CartCoordinate CASM::Coordinate::cart ( )

inlineinherited

Set Cartesian coordinate vector and update fractional coordinate vector.

Definition at line 593 of file Coordinate.hh.

const vector_type& CASM::Coordinate::cart ( ) const

inlineinherited

const Access the Cartesian coordinate vector

Definition at line 87 of file Coordinate.hh.

Coordinate_impl::CartCoordinateComponent CASM::Coordinate::cart ( Coordinate::size_type index )

inlineinherited

Set a component of the Cartesian coordinate vector.

Definition at line 599 of file Coordinate.hh.

const double& CASM::Coordinate::cart ( size_type index ) const

inlineinherited

const Access a component of the Cartesian coordinate vector

Definition at line 100 of file Coordinate.hh.

bool CASM::Coordinate::compare	(	const Coordinate &	RHS,
		double	tol = `TOL`
	)		const

inherited

Returns true if this->min_dist(RHS)<tol.

Definition at line 73 of file Coordinate.cc.

bool CASM::Coordinate::compare	(	const Coordinate &	RHS,
		Coordinate &	translation,
		double	tol = `TOL`
	)		const

inherited

Returns true if this->min_dist(RHS)<tol if true, calculates

Parameters

translation such that *this = (RHS+translation)

Definition at line 80 of file Coordinate.cc.

bool CASM::Coordinate::compare_type ( const Coordinate & RHS ) const

inherited

Return true – Exists to allow duck-typing with Site.

Definition at line 86 of file Coordinate.cc.

const vector_type& CASM::Coordinate::const_cart ( ) const

inlineinherited

user override to force const Access the Cartesian coordinate vector

Definition at line 92 of file Coordinate.hh.

const double& CASM::Coordinate::const_cart ( size_type index ) const

inlineinherited

const Access a component of the Cartesian coordinate vector

Definition at line 105 of file Coordinate.hh.

const vector_type& CASM::Coordinate::const_frac ( ) const

inlineinherited

user override to force const Access the fractional coordinate vector

Definition at line 66 of file Coordinate.hh.

const double& CASM::Coordinate::const_frac ( size_type index ) const

inlineinherited

user override to force const Access the fractional coordinate vector

Definition at line 79 of file Coordinate.hh.

double CASM::Coordinate::dist ( const Coordinate & neighbor ) const

inherited

distance (in Angstr) of neighbor from *this

Definition at line 146 of file Coordinate.cc.

Coordinate_impl::FracCoordinate CASM::Coordinate::frac ( )

inlineinherited

Set the fractional coordinate vector.

Definition at line 581 of file Coordinate.hh.

const vector_type& CASM::Coordinate::frac ( ) const

inlineinherited

const Access the fractional coordinate vector

Definition at line 61 of file Coordinate.hh.

Coordinate_impl::FracCoordinateComponent CASM::Coordinate::frac ( Coordinate::size_type index )

inlineinherited

Set a component of the fractional coordinate vector.

Definition at line 587 of file Coordinate.hh.

const double& CASM::Coordinate::frac ( size_type index ) const

inlineinherited

const Access a component of the fractional coordinate vector

Definition at line 74 of file Coordinate.hh.

void CASM::Coordinate::from_json ( const jsonParser & json )

inherited

Definition at line 398 of file Coordinate.cc.

const Lattice& CASM::Coordinate::home ( ) const

inlineinherited

Access the home lattice of the coordinate.

Definition at line 195 of file Coordinate.hh.

bool CASM::Coordinate::is_lattice_shift ( double tol = TOL ) const

inherited

Checks to see if coordinate is at a lattice translation with respect to the origin.

Definition at line 367 of file Coordinate.cc.

bool CASM::Coordinate::is_within ( ) const

inherited

Checks to see if coordinate is in the unit cell, but does not translate it.

Definition at line 301 of file Coordinate.cc.

double CASM::Coordinate::min_dist ( const Coordinate & neighbor ) const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

Is unsafe if min_dist is comparable to half a lattice vector in length

Definition at line 155 of file Coordinate.cc.

double CASM::Coordinate::min_dist	(	const Coordinate &	neighbor,
		Coordinate &	translation
	)		const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

This version calculates the translation such that (neighbor+translation) is the periodic nearest period image of neighbor

Definition at line 169 of file Coordinate.cc.

double CASM::Coordinate::min_dist2	(	const Coordinate &	neighbor,
		const Eigen::Ref< const Eigen::Matrix3d > &	metric
	)		const

inherited

Finds same shift as min_dist but returns shift(CART).transpose()*metric*shift(CART)

Definition at line 205 of file Coordinate.cc.

bool CASM::Coordinate::operator!= ( const Coordinate & RHS ) const

inlineinherited

Definition at line 120 of file Coordinate.hh.

Coordinate & CASM::Coordinate::operator+= ( const Coordinate & RHS )

inherited

Positive translation of this coordinate by RHS.cart()

Definition at line 38 of file Coordinate.cc.

Coordinate CASM::Coordinate::operator- ( ) const

inherited

unary minus of this coordinate

Definition at line 53 of file Coordinate.cc.

Coordinate & CASM::Coordinate::operator-= ( const Coordinate & RHS )

inherited

Negative translation of this coordinate by RHS.cart()

Definition at line 45 of file Coordinate.cc.

bool CASM::Coordinate::operator== ( const Coordinate & RHS ) const

inherited

Definition at line 59 of file Coordinate.cc.

void CASM::Coordinate::print	(	std::ostream &	stream,
		COORD_TYPE	mode,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

inherited

Definition at line 112 of file Coordinate.cc.

void CASM::Coordinate::print	(	std::ostream &	stream,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

inherited

Definition at line 107 of file Coordinate.cc.

void CASM::Coordinate::print_axis	(	std::ostream &	stream,
		COORD_TYPE	mode,
		char	term = `0`,
		int	prec = `7`,
		int	pad = `5`
	)		const

inherited

Print normalized vector.

Definition at line 129 of file Coordinate.cc.

void CASM::Coordinate::read	(	std::istream &	stream,
		COORD_TYPE	mode
	)

inherited

Definition at line 92 of file Coordinate.cc.

double CASM::Coordinate::robust_min_dist ( const Coordinate & neighbor ) const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

It is safe in all cases, because it uses the lattice Wigner-Seitz cell to determine the nearest image, but this makes it slower than min_dist

Definition at line 179 of file Coordinate.cc.

double CASM::Coordinate::robust_min_dist	(	const Coordinate &	neighbor,
		Coordinate &	translation
	)		const

inherited

Returns distance (in Angstr) to nearest periodic image of neighbor.

This version calculates the translation such that (neighbor+translation) is the periodic nearest period image of neighbor It is safe in all cases, because it uses the lattice Wigner-Seitz cell to determine the nearest image, but this makes it slower than min_dist

Definition at line 190 of file Coordinate.cc.

void CASM::Coordinate::set_basis_ind ( Index _basis_ind )

inlineinherited

Set basis Index.

Definition at line 185 of file Coordinate.hh.

void CASM::Coordinate::set_lattice	(	const Lattice &	new_lat,
		COORD_TYPE	mode
	)

inherited

Change the home lattice of the coordinate, selecting one representation (either CART or FRAC) that remains invariant.

Parameters

invariant_mode

invariant_mode == CART: Cartesian coordinates stay the same, and fractional coordinates are updated Ex: (my_coord.set_lattice(superlattice, CART); // this is how superlattices get filled.

invariant_mode == FRAC: Fractional coordinates stay the same, and Cartesian coordinates are updated Ex: you can apply a strain by changing the lattice and keepin FRAC invariant (my_coord.set_lattice(strained_lattice, FRAC); Ex: you can apply a rotation by changing the lattice and keeping FRAC invariant (my_coord.set_lattice(rotated_lattice, FRAC);

Definition at line 245 of file Coordinate.cc.

jsonParser & CASM::Coordinate::to_json ( jsonParser & json ) const

inherited

Definition at line 383 of file Coordinate.cc.

int CASM::Coordinate::voronoi_number ( ) const

inherited

Number of periodic images of this coordinate that are on voronoi cell boundary of its home lattice

Definition at line 317 of file Coordinate.cc.

int CASM::Coordinate::voronoi_number ( const Lattice & cell ) const

inherited

Number of periodic images of this coordinate that are on voronoi cell boundary of 'cell'

Definition at line 325 of file Coordinate.cc.

bool CASM::Coordinate::voronoi_within ( )

inherited

Map coordinate into the voronoi cell using a lattice translation.

Definition at line 333 of file Coordinate.cc.

bool CASM::Coordinate::voronoi_within ( Coordinate & translation )

inherited

Same as voronoi_within(), but lattice translation is stored in Coordinate translation such that coord_after = coord_before + translation returns true if *this was already within the voronoi cell

Definition at line 348 of file Coordinate.cc.

bool CASM::Coordinate::within ( )

inherited

Map coordinate into the unit cell using a lattice translation returns true if *this was already within the unit cell

Definition at line 261 of file Coordinate.cc.

bool CASM::Coordinate::within ( Coordinate & translation )

inherited

Same as within(), but lattice translation is stored in Coordinate translation, such that coord_after = coord_before + translation returns true if *this was already within the unit cell

Definition at line 280 of file Coordinate.cc.

The documentation for this class was generated from the following files:

/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/include/casm/crystallography/Molecule.hh
/Users/bpuchala/Work/codes/CASMcode_v0.2.X_reference/src/casm/crystallography/Molecule.cc

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Member Typedef Documentation

Member Function Documentation